A,Y29tLz9hPTQ2JmM9NDQzNzgmczE9Q0,123
B,FJNLTA2MjQyMDE3LVAmczI9ODQ3MDA,321

A,result of base 64 decode,123
B,result of base 64 decode,321

awk -F',' -v OFS=',' '"echo "$2" | base64" | getline $2' file

kent$  cat f
A,Y29tLz9hPTQ2JmM9NDQzNzgmczE9Q0,123
B,FJNLTA2MjQyMDE3LVAmczI9ODQ3MDA,321

kent$  awk -F',' -v OFS=',' '"echo "$2" | base64" | getline $2' f
A,WTI5dEx6OWhQVFEySm1NOU5EUXpOemdtY3pFOVEwCg==,123
B,RkpOTFRBMk1qUXlNREUzTFZBbWN6STlPRFEzTURBCg==,321